Molecular Dynamics and Other HPC Simulations for Drug Discovery

High performance computing (HPC) is taking an increasingly important place in drug discovery. It makes possible the simulation of complex biochemical systems with high precision in a short time, thanks to the use of sophisticated algorithms. It promotes the advancement of knowledge in fields that are inaccessible or difficult to access through experimentation and it contributes to accelerating the discovery of drugs for unmet medical needs while reducing costs. Herein, we report how computational performance has evolved over the past years, and then we detail three domains where HPC is essential. Molecular dynamics (MD) is commonly used to explore the flexibility of proteins, thus generating a better understanding of different possible approaches to modulate their activity. Modeling and simulation of biopolymer complexes enables the study of protein-protein interactions (PPI) in healthy and disease states, thus helping the identification of targets of pharmacological interest. Virtual screening (VS) also benefits from HPC to predict in a short time, among millions or billions of virtual chemical compounds, the best potential ligands that will be tested in relevant assays to start a rational drug design process.

Artificial Intelligence, Machine Learning, and Deep Learning in Real-Life Drug Design Cases

The discovery and development of drugs is a long and expensive process with a high attrition rate. Computational drug discovery contributes to ligand discovery and optimization, by using models that describe the properties of ligands and their interactions with biological targets. In recent years, artificial intelligence (AI) has made remarkable modeling progress, driven by new algorithms and by the increase in computing power and storage capacities, which allow the processing of large amounts of data in a short time. This review provides the current state of the art of AI methods applied to drug discovery, with a focus on structure- and ligand-based virtual screening, library design and high-throughput analysis, drug repurposing and drug sensitivity, de novo design, chemical reactions and synthetic accessibility, ADMET, and quantum mechanics.

Fine tuning for success in structure-based virtual screening

Structure-based virtual screening plays a significant role in drug-discovery. The method virtually docks millions of compounds from corporate or public libraries into a binding site of a disease-related protein structure, allowing for the selection of a small list of potential ligands for experimental testing. Many algorithms are available for docking and assessing the affinity of compounds for a targeted protein site. The performance of affinity estimation calculations is highly dependent on the size and nature of the site, therefore a rationale for selecting the best protocol is required. To address this issue, we have developed an automated calibration process, implemented in a Knime workflow. It consists of four steps: preparation of a protein test set with structures and models of the target, preparation of a compound test set with target-related ligands and decoys, automatic test of 24 scoring/rescoring protocols for each target structure and model, and graphical display of results. The automation of the process combined with execution on high performance computing resources greatly reduces the duration of the calibration phase, and the test of many combinations of algorithms on various target conformations results in a rational and optimal choice of the best protocol. Here, we present this tool and exemplify its application in setting-up an optimal protocol for SBVS against Retinoid X Receptor alpha.

Prevalence of stroke in Argentina: A door-to-door population-based study (EstEPA)

BACKGROUND

Stroke burden is highest and is still rising in low- and middle-income countries. Epidemiologic stroke data are lacking in many of these countries. Stroke prevalence in Argentina has been unexplored for almost three decades.

AIM

This population-based study aims to determine prevalence of stroke in a representative sample of the Argentinean population.

METHODS

We performed a door-to-door survey of randomly selected households in a city of 18,650 inhabitants. A structured questionnaire screening for potential stroke cases was used. All subjects screened positive were then evaluated by stroke neurologists for final adjudication. Data about stroke subtypes, neurological status, vascular risk factors, medications, and diagnostic tests were also collected.

RESULTS

Among 2156 surveys, 294 were screened positive for a possible stroke. After neurological evaluation, there were 41 confirmed cases. The adjusted stroke prevalence was 1,974/100,000 inhabitants older than 40 years, and it was higher in men than in women (26.3‰ vs 13.2‰, p<0.01). Prevalence of ischemic stroke, intracranial hemorrhage, and transient ischemic attack were 15.8‰, 2.93‰, and 2.93‰, respectively. The most prevalent vascular risk factors in stroke survivors were hypertension, obstructive sleep apnea, and dyslipidemia.

CONCLUSION

Approximately 2 in every 100 subjects older than 40 years in this population are stroke survivors. Stroke prevalence in Argentina has remained stable over the last 30 years; it is higher than in most Latin American countries and similar to western populations.

User-Friendly Quantum Mechanics: Applications for Drug Discovery

Quantum mechanics (QM) methods provide a fine description of receptor-ligand interactions and of chemical reactions. Their use in drug design and drug discovery is increasing, especially for complex systems including metal ions in the binding sites, for the design of highly selective inhibitors, for the optimization of bi-specific compounds, to understand enzymatic reactions, and for the study of covalent ligands and prodrugs. They are also used for generating molecular descriptors for predictive QSAR/QSPR models and for the parameterization of force fields. Thanks to the continuous increase of computational power offered by GPUs and to the development of sophisticated algorithms, QM methods are becoming part of the standard tools used in computer-aided drug design (CADD). We present the most used QM methods and software packages, and we discuss recent representative applications in drug design and drug discovery.

Clinical, metabolic and psychological outcomes and treatment costs of a prospective randomized trial based on different educational strategies to improve diabetes care (PRODIACOR)

AIM

To evaluate the effect of system interventions (formalized data collection and 100% coverage of medications and supplies) combined with physician and/or patient education on therapeutic indicators and costs in Type 2 diabetes.

METHODS

This was a randomized 2 × 2 design in public health, social security or private prepaid primary care clinics in Corrientes, Argentina. Thirty-six general practitioners and 468 adults with Type 2 diabetes participated. Patients of nine participating physicians were selected randomly and assigned to one of four structured group education programmes (117 patients each): control (group 1), physician education (group 2), patient education (group 3), and both physician education and patient education (group 4), with identical system interventions in all four groups. Outcome measures included HbA(1c), BMI, blood pressure, fasting glucose, lipid profile, drug consumption, resource use and patient well-being at baseline and every 6 months up to 42 months.

RESULTS

HbA(1c) decreased significantly from 4 mmol/mol to 10 mmol/mol by 42 months (P < 0.05); the largest and more consistent decrease was in the groups where patients and physicians were educated. Blood pressure and triglycerides decreased significantly in all groups; the largest changes were recorded in the combined education group. The World Health Organization-5 Lowe score showed significant improvements, without differences among groups. The lowest treatment cost was seen in the combined education group.

CONCLUSIONS

In a primary care setting, educational interventions combined with comprehensive care coverage resulted in long-term improvement in clinical, metabolic and psychological outcomes at the best cost-effectiveness ratio.

Low plasma leptin concentration and low rates of fat oxidation in weight-stable post-obese subjects

OBJECTIVE

A low resting metabolic rate for a given body size and composition, a low rate of fat oxidation, low levels of physical activity, and low plasma leptin concentrations are all risk factors for body weight gain. The aim of the present investigation was to compare resting metabolic rate (RMR), respiratory quotient (RQ), levels of physical activity, and plasma leptin concentrations in eight post-obese adults (2 males and 6 females; 48.9 +/- 12.2 years; body mass index [BMI]: 24.5 +/- 1.0 kg/m2; body fat 33 +/- 5%; mean +/- SD) who lost 27.1 +/- 21.3 kg (16 to 79 kg) and had maintained this weight loss for > or =2 months (2 to 9 months) to eight age- and BMI-matched control never-obese subjects (1 male and 7 females; 49.1 +/- 5.2 years; BMI 24.4 +/- 1.0 kg/m2; body fat 33 +/- 7%).

RESEARCH METHODS AND PROCEDURES

Following 3 days of weight maintenance diet (50% carbohydrate and 30% fat), RMR and RQ were measured after a 10-hour fast using indirect calorimetry and plasma leptin concentrations were measured using radioimmunoassay. Levels of physical activity were estimated using an accelerometer over a 48-hour period in free living conditions.

RESULTS

After adjustment for fat mass and fat-free mass, post-obese subjects had, compared with controls, similar levels of physical activity (4185 +/- 205 vs. 4295 +/- 204 counts) and similar RMR (1383 +/- 268 vs. 1430 +/- 104 kcal/day) but higher RQ (0.86 +/- 0.04 vs. 0.81 +/- 0.03, p < 0.05). Leptin concentration correlated positively with percent body fat (r = 0.57, p < 0.05) and, after adjusting for fat mass and fat-free mass, was lower in post-obese than in control subjects (4.5 +/- 2.1 vs. 11.6 +/- 7.9 ng/mL, p < 0.05).

DISCUSSION

The low fat oxidation and low plasma leptin concentrations observed in post-obese individuals may, in part, explain their propensity to relapse.

Sealant status and factors associated with sealant presence among children in Milwaukee, WI

To determine the percent of school-children aged 6-14 years with sealants placed in their permanent molars in the City of Milwaukee. 2) To describe factors associated with sealant presence among these children. 3) To describe differences, if any, among ethnic majority and minority groups. Twelve public schools agreed to participate in this project. After consent forms were obtained, 1,234 dental exams were performed. A 15-item pretested questionnaire was given to each child to take home for the parent(s) to complete. Response rate was 60 percent (N = 742). Data were analyzed using frequencies and Chi-Square tests (P-value < 0.05). Only 9.6 percent of the sample had sealants on their permanent molars. Variables that were found associated with children more likely to have sealants included: gender (female children more likely than males); children with a recent dental exam; children having a regular dentist; parents having heard about sealants before this study; parents' correct knowledge regarding the purpose of sealants; higher level of parents' education; higher parents' total annual income; ethnicity (Caucasian children more likely than Hispanic, African American, American Indian, or Asian children); and age (children in the older group, 10-14 years, more likely than children in the younger group, 6-9 years). Percent of school-children with sealants on their permanent molars in the city of Milwaukee is low. Efforts are needed to increase the knowledge of sealants by the general public as well as to promote sealant use by dentists in both private practice and public health programs, especially for minority children.

Craniometric measurements of craniofacial malformations in the X-linked hypophosphatemic (Hyp) mouse on two different genetic backgrounds: C57BL/6J and B6C3H

This study reports data on craniometric measurements in the X-linked hypophosphatemic (Hyp) mouse on two different genetic backgrounds: C57BL/6J and B6C3H. Heads of normal females "+/+," normal males "+/Y," heterozygous mutant females "Hyp/+," and hemizygous mutant males "Hyp/Y" for each genetic background were examined. Data were collected via skull measurements. On a C57BL/6J background, the neurocranium of mutants "Hyp/+" and "Hyp/Y" was shorter and slightly higher than in normal counterparts. On a B6C3H background, mutant mice "Hyp/+" and "Hyp/Y" were shorter in neurocranial length than in normal counterparts. Viscerocranial height was larger in "Hyp/Y" than in normal counterparts. No differences in neurocranial and mandibular height were found. Mutant mice on a C57BL/6J background were compared to mutant mice on a B6C3H background. No differences in neurocranial length were found. Cranial length was shorter in "Hyp/Y" on C57BL/6J than in "Hyp/+" on B6C3H. Facial length parameters were shorter in "Hyp/Y" on C57BL/6J than in "Hyp/Y" and "Hyp/+" mutant mice on B6C3H. Mandibular length was shorter in "Hyp/Y" on C57BL/6J than in "Hyp/+" on C57BL/6J and both mutant mice ("Hyp/Y" and "Hyp/+") on a B6C3H background. The results of this study indicate that craniofacial growth is less affected in mutant mice on a B6C3H genetic background than in mutant mice on a C57BL/6J genetic background.

Sealant use by general practitioners: a Minnesota survey

A 1987 random-sample mail survey on the use of sealants by general dentists in Minnesota (71 percent response, N = 375) found that almost all (95 percent) reported using sealants. Usage was predominantly for the six- to fourteen-year-old patient age-group. Frequency of use per week ranged from 1-25 (mean +/- S.D. = 3.3 +/- 3.6). More frequent use was associated positively with employing more dental hygienists, having more sources of information about sealants, having higher knowledge scores, and having more favorable opinions about sealants. While reported use of sealants is high in this state, the frequency of use and proportion of child patients receiving sealants were both relatively low.

Sealant knowledge and use by pediatric dentists: 1987 Minnesota survey

Sealants are safe, cost-effective, and easy to apply. All of the pediatric dentists surveyed in this study reported using sealants. Only 46 percent, however, applied sealants more than ten times per week. Sealant use was most often for the six- to fourteen-year-old age-group.